Real-Time Genome Identification via Probabilistic Sequence Matching
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Solution Overview
Problem
Current methods for identifying DNA or RNA sequences in bioterrorism scenarios or epidemics are slow and require extensive resources, hindering rapid and accurate identification of pathogens, which is critical for timely response and containment.
Innovation Solution
A system and method utilizing probabilistic data matching in handheld or larger electronic devices to generate and compare nucleic acid sequence information in real-time with a database, enabling rapid identification of organisms, including pathogens, through sequential fragment comparison and amplification, using techniques like Bayesian approaches for accurate species and strain detection.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional DNA sequencing methods (Sanger method, sequencing-by-hybridization, sequencing-by-synthesis) are used, then sequence information can be obtained, but the process is slow and requires extensive resources
Solution Approach 1:
The patent segments the DNA sequence into multiple short reads (fragments) that can be independently sequenced and processed. This segmentation enables parallel processing of multiple sequence fragments simultaneously, dramatically reducing the total time required for complete genome identification while maintaining accuracy through probabilistic matching of all fragments against reference databases.
Solution Approach 2:
The patent performs preliminary probabilistic matching of short sequence reads against reference genome databases during the sequencing process itself, rather than waiting for complete sequence assembly. This preliminary action enables real-time identification of pathogens as sequence data is being generated, significantly reducing detection time while maintaining high accuracy through cumulative probability calculations.
2Measurement precision
If traditional DNA sequencing methods are used, then sequence information can be obtained, but extensive resources and multiple people are required
Solution Approach 1:
The patent replaces complex mechanical and manual sequencing operations with automated next-generation sequencing technology combined with computational probabilistic matching. This substitution eliminates the need for extensive manual intervention and complex laboratory infrastructure, reducing device complexity and resource requirements while maintaining or improving identification accuracy through algorithmic analysis.
Solution Approach 2:
The patent creates multiple copies of the target DNA through amplification methods (such as PCR or whole genome amplification) before sequencing. This copying enables sufficient material to be available for multiple parallel sequencing reactions, reducing the need for repeated sampling and extensive resources while maintaining statistical accuracy through analysis of multiple sequence copies.
3Productivity
If short sequence reads are used for identification, then sequencing speed increases, but identification accuracy may decrease
Solution Approach 1:
The patent merges the results of multiple independent short read matches against the reference database, combining their individual probability scores into a cumulative identification result. This merging approach maintains high sequencing speed by using short reads while recovering accuracy through the aggregated statistical evidence from multiple fragment matches, demonstrating that the sum of many short-read probabilities yields confident species identification.
Data Source
AI summary
The present invention belongs to the field of genomics and nucleic acid sequencing. It involves a novel method of sequencing biological material and real-time probabilistic matching of short strings of sequencing information to identify all species present in said biological material. It is related to real-time probabilistic matching of sequence information, and more particular to comparing short strings of a plurality of sequences of single molecule nucleic acids, whether amplified or unamplied, whether chemically synthesized or physically interrogated, as fast as the sequence information is generated and in parallel with continuous sequence information generation or collection.